Structural basis for semaphorin signalling through the plexin receptor

Nature

Volumn 467, Issue 7319, 2010, Pages 1123-1127

  Nogi, Terukazu ^a   Yasui, Norihisa ^a,c   Mihara, Emiko ^a   Matsunaga, Yukiko ^a   Noda, Masanori ^a   Yamashita, Naoya ^b   Toyofuku, Toshihiko ^a   Uchiyama, Susumu ^a   Goshima, Yoshio ^b   Kumanogoh, Atsushi ^a   Takagi, Junichi ^a  

^a OSAKA UNIVERSITY   (Japan)

^b YOKOHAMA CITY UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; HETERODIMER; HOMODIMER; MONOMER; PLEXIN; SEMAPHORIN;

CELL ORGANELLE; ENZYME ACTIVITY; LIGAND; MEASUREMENT METHOD; MEMBRANE; MOLECULAR ANALYSIS; MUTATION; PHYSIOLOGY; PROTEIN; SIGNALING;

ARTICLE; CELL ACTIVITY; CELL SURFACE; COMPLEX FORMATION; CRYSTAL STRUCTURE; CYTOPLASM; EMBRYO; HUMAN; HUMAN CELL; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; HEK293 CELLS; HUMANS; LIGANDS; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NERVE TISSUE PROTEINS; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, CELL SURFACE; SEMAPHORINS; SIGNAL TRANSDUCTION; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 78049370988     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature09473     Document Type: Article

References (41)

1. Tamagnone, L. & Comoglio, P.M.To move or not to move? Semaphorin signalling in cell migration. EMBO Rep. 5, 356-361 (2004).
2. Zhou, Y., Gunput, R. A. & Pasterkamp, R. J. Semaphorin signaling: progress made and promises ahead. Trends Biochem. Sci. 33, 161-170 (2008).
3. Suzuki, K., Kumanogoh, A. & Kikutani, H. Semaphorins and their receptors in immune cell interactions. Nature Immunol. 9, 17-23 (2008).
4. Neufeld, G. & Kessler, O. The semaphorins: versatile regulators of tumour progression and tumour angiogenesis. Nature Rev. Cancer 8, 632-645 (2008).
5. Antipenko, A. et al. Structure of the semaphorin-3A receptor binding module. Neuron 39, 589-598 (2003).
6. Love, C. A. et al. The ligand-binding face of the semaphorins revealed by the high-resolution crystal structure of SEMA4D. Nature Struct. Biol. 10, 843-848 (2003).
7. Stamos, J., Lazarus, R. A., Yao, X., Kirchhofer, D. &Wiesmann, C. Crystal structure of the HGF b-chain in complex with the Sema domain of the Met receptor. EMBO J. 23, 2325-2335 (2004).
8. Suto, F. et al. Plexin-A4 mediates axon-repulsive activities of both secreted and transmembrane semaphorins and plays rolesin nerve fiber guidance. J.Neurosci. 25, 3628-3637 (2005).
9. Renaud, J. et al. Plexin-A2 and its ligand, Sema6A, control nucleus-centrosome coupling in migrating granule cells. Nature Neurosci. 11, 440-449 (2008).
10. Merte, J. et al. A forward genetic screenin mice identifies Sema3A(K108N), which binds to neuropilin-1 but cannot signal. J. Neurosci. 30, 5767-5775 (2010).
11. Xu, X. M. et al. The transmembrane protein semaphorin 6A repels embryonic sympathetic axons. J. Neurosci. 20, 2638-2648 (2000).
12. LeDu, M.H., Stigbrand, T., Taussig, M.J., Menez, A.& Stura, E. A.Crystal structure of ? alkaline phosphatase from human placenta at 1.8A resolution. Implication for a substrate specificity. J. Biol. Chem. 276, 9158-9165 (2001).
13. Tong, Y. et al. Binding ofRac1, Rnd1, and RhoD to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain. J. Biol. Chem. 282, 37215-37224 (2007).
14. Takahashi, T. & Strittmatter, S. M. Plexina1 autoinhibition by the plexin sema domain. Neuron 29, 429-439 (2001).
15. Chaudhry, C., Weston, M. C., Schuck, P., Rosenmund, C. & Mayer, M. L. Stability of ligand-binding domain dimer assembly controls kainate receptor desensitization. EMBO J. 28, 1518-1530 (2009).
16. Niemann, H. H. et al. Structure of the human receptor tyrosine kinase met in complex with the Listeria invasion protein InlB. Cell 130, 235-246 (2007).
17. Luo, B. H. & Springer, T. A. Integrin structures and conformational signaling. Curr. Opin. Cell Biol. 18, 579-586 (2006).
18. Oinuma, I., Ishikawa, Y., Katoh, H. & Negishi, M. The Semaphorin 4D receptor Plexin-B1 is a GTPase activating protein for R-Ras. Science 305, 862-865 (2004).
19. He, H., Yang, T., Terman, J. R. & Zhang, X. Crystal structure of the plexin A3 intracellular region reveals an autoinhibited conformation through active site sequestration. Proc. Natl Acad. Sci. USA 106, 15610-15615 (2009).
20. Tong, Y. et al. Structure and function of the intracellular region of the plexin-B1 transmembrane receptor. J. Biol. Chem. 284, 35962-35972 (2009).
21. Liu, H. et al. Structural basis of semaphorin-plexin recognition and viral mimicry from Sema7A and A39R complexes with plexinC1. Cell 142, 749-761 (2010).
22. Stanley, P. Chinese hamster ovary cell mutants with multiple glycosylation defects for production of glycoproteins with minimal carbohydrate heterogeneity. Mol. Cell. Biol. 9, 377-383 (1989).
23. Tabata, S. et al. A rapid screening method for cell lines producing singly-tagged recombinant proteins using the "TARGET tag" system. J. Proteomics 73, 1777-1785 (2010).
24. Toyofuku, T. et al. Repulsive and attractive semaphorins cooperate to direct the navigation of cardiac neural crest cells. Dev. Biol. 321, 251-262 (2008).
25. Goshima, Y. et al. A novel action of collapsin: collapsin-1 increases antero-and retrograde axoplasmic transport independently of growth cone collapse. J. Neurobiol. 33, 316-328 (1997).
26. Leahy, D. J., Dann, C. E. III, Longo, P., Perman, B. & Ramyar, K. X. A mammalian expression vector for expression and purification of secreted proteins for structural studies. Protein Expr. Purif. 20, 500-506 (2000).
27. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
28. Vagin, A. & Teplyakov, A. MOLREP: an automated program for molecular replacement. J. Appl. Cryst. 30, 1022-1025 (1997).
29. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004).
30. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240-255 (1997).
31. Davis, I. W. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375-W383 (2007).
32. Perrakis, A., Harkiolaki, M., Wilson, K. S. & Lamzin, V. S. ARP/wARP and molecular replacement. Acta Crystallogr. D 57, 1445-1450 (2001).
33. Schneider, T. R. & Sheldrick, G. M. Substructure solution with SHELXD. Acta Crystallogr. D 58, 1772-1779 (2002).
34. Bricogne, G., Vonrhein, C., Flensburg, C., Schiltz, M. & Paciorek, W. Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Crystallogr. D 59, 2023-2030 (2003).
35. Abrahams, J. P. & Leslie, A. G. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallogr. D 52, 30-42 (1996).
36. Lee, B. & Richards, F. M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379-400 (1971).
37. Krissinel, E. & Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D 60, 2256-2268 (2004).
38. DeLano, W. L. The PyMOL Molecular Graphics System (DeLano Scientific, 2002).
39. Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA 98, 10037-10041 (2001).
40. Schuck, P. Size-distribution analysisofmacromolecules bysedimentation velocity ultracentrifugation and Lamm equation modeling. Biophys. J. 78, 1606-1619 (2000).
41. Schuck, P. On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation. Anal. Biochem. 320, 104-124 (2003).